Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 14L4Z

Calculation Name: 3P5J-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3P5J

Chain ID: B

ChEMBL ID:

UniProt ID: Q9CWY8

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1815223.542693
FMO2-HF: Nuclear repulsion 1744364.15213
FMO2-HF: Total energy -70859.390563
FMO2-MP2: Total energy -71069.288343


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(B:11:ALA)


Summations of interaction energy for fragment #1(B:11:ALA)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
1.4753.572-0.003-0.969-1.1240.004
Interaction energy analysis for fragmet #1(B:11:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.059 / q_NPA : 0.030
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3B13ARG10.9300.9573.8410.7032.5040.000-0.944-0.8560.004
4B14GLN00.0110.0054.1450.4860.689-0.001-0.014-0.1880.000
5B15LEU0-0.049-0.0377.366-0.008-0.0080.0000.0000.0000.000
6B16VAL00.0400.03911.1800.0760.0760.0000.0000.0000.000
7B17PHE00.016-0.01613.343-0.015-0.0150.0000.0000.0000.000
8B18LEU0-0.0080.01616.6160.0320.0320.0000.0000.0000.000
9B19LEU00.011-0.00419.243-0.012-0.0120.0000.0000.0000.000
10B20PRO00.0100.01022.3760.0140.0140.0000.0000.0000.000
11B21GLU-1-0.753-0.86125.264-0.067-0.0670.0000.0000.0000.000
12B22HIS00.000-0.00626.4310.0050.0050.0000.0000.0000.000
13B23LEU0-0.066-0.04723.6180.0010.0010.0000.0000.0000.000
14B24LYS10.8110.90522.6320.0580.0580.0000.0000.0000.000
15B25ASP-1-0.818-0.86924.819-0.055-0.0550.0000.0000.0000.000
16B26ALA0-0.004-0.02427.978-0.007-0.0070.0000.0000.0000.000
17B27SER0-0.068-0.05829.5790.0010.0010.0000.0000.0000.000
18B28LYS10.7830.88927.0800.1030.1030.0000.0000.0000.000
19B29LYS10.8860.93532.9770.0600.0600.0000.0000.0000.000
20B30LYS11.0131.02632.8510.0590.0590.0000.0000.0000.000
21B31LYS10.8900.92030.3320.0760.0760.0000.0000.0000.000
22B32LYS10.9610.99125.7930.0750.0750.0000.0000.0000.000
23B33SER00.0340.02524.826-0.004-0.0040.0000.0000.0000.000
24B34SER0-0.005-0.03425.2740.0020.0020.0000.0000.0000.000
25B35LEU00.0050.01920.8310.0060.0060.0000.0000.0000.000
26B36LEU00.0150.00523.384-0.009-0.0090.0000.0000.0000.000
27B37PHE00.0230.01318.5710.0030.0030.0000.0000.0000.000
28B38VAL0-0.018-0.00522.250-0.002-0.0020.0000.0000.0000.000
29B39LYS10.8830.92721.5280.3060.3060.0000.0000.0000.000
30B40LEU0-0.027-0.00525.8100.0160.0160.0000.0000.0000.000
31B41ALA00.0490.01428.672-0.011-0.0110.0000.0000.0000.000
32B42ASN0-0.0010.00628.3620.0130.0130.0000.0000.0000.000
33B43PRO0-0.007-0.00930.9720.0070.0070.0000.0000.0000.000
34B44HIS0-0.049-0.01632.1860.0040.0040.0000.0000.0000.000
35B45SER00.022-0.00932.7820.0070.0070.0000.0000.0000.000
36B46GLY00.0300.02730.249-0.010-0.0100.0000.0000.0000.000
37B47GLU-1-0.917-0.96928.555-0.184-0.1840.0000.0000.0000.000
38B48GLY0-0.051-0.03827.6820.0040.0040.0000.0000.0000.000
39B49ALA00.0040.01625.030-0.008-0.0080.0000.0000.0000.000
40B50THR0-0.072-0.04420.321-0.012-0.0120.0000.0000.0000.000
41B51TYR00.0600.03723.6010.0090.0090.0000.0000.0000.000
42B52LEU0-0.0120.00221.691-0.016-0.0160.0000.0000.0000.000
43B53ILE00.0220.01224.5510.0160.0160.0000.0000.0000.000
44B54ASP-1-0.741-0.86726.797-0.117-0.1170.0000.0000.0000.000
45B55MET00.0150.00728.0140.0100.0100.0000.0000.0000.000
46B56CYS0-0.095-0.03728.7410.0070.0070.0000.0000.0000.000
47B57LEU0-0.015-0.00130.9240.0090.0090.0000.0000.0000.000
48B58GLN0-0.056-0.01732.0230.0070.0070.0000.0000.0000.000
49B59GLN00.0660.03230.8060.0010.0010.0000.0000.0000.000
50B60LEU00.0020.00428.803-0.007-0.0070.0000.0000.0000.000
51B61PHE00.0280.00825.6620.0090.0090.0000.0000.0000.000
52B62GLU-1-0.784-0.86826.339-0.177-0.1770.0000.0000.0000.000
53B63ILE0-0.058-0.03419.601-0.002-0.0020.0000.0000.0000.000
54B64LYS10.8890.95422.5830.1550.1550.0000.0000.0000.000
55B65VAL0-0.020-0.02817.380-0.015-0.0150.0000.0000.0000.000
56B66PHE00.0140.02818.4920.0120.0120.0000.0000.0000.000
57B67LYS10.8240.86815.6670.3190.3190.0000.0000.0000.000
58B68GLU-1-0.806-0.86718.999-0.130-0.1300.0000.0000.0000.000
59B69LYS10.9050.93718.7310.1490.1490.0000.0000.0000.000
60B70HIS00.005-0.00617.662-0.010-0.0100.0000.0000.0000.000
61B71HIS00.0480.03315.8310.0200.0200.0000.0000.0000.000
62B72SER0-0.077-0.05710.830-0.065-0.0650.0000.0000.0000.000
63B73TRP0-0.010-0.00210.0370.0830.0830.0000.0000.0000.000
64B74PHE00.0390.0179.485-0.024-0.0240.0000.0000.0000.000
65B75ILE0-0.017-0.0137.730-0.070-0.0700.0000.0000.0000.000
66B76ASN00.0110.0168.4750.1010.1010.0000.0000.0000.000
67B77GLN00.0230.0219.298-0.078-0.0780.0000.0000.0000.000
68B78SER0-0.035-0.0234.6130.1500.228-0.001-0.007-0.0700.000
69B79VAL00.0490.0205.278-0.194-0.1940.0000.0000.0000.000
70B80GLN0-0.019-0.0024.868-0.707-0.692-0.001-0.004-0.0100.000
71B81SER00.0470.0166.9190.1540.1540.0000.0000.0000.000
72B82GLY00.0070.0079.434-0.106-0.1060.0000.0000.0000.000
73B83GLY00.0670.03611.6240.0680.0680.0000.0000.0000.000
74B84LEU0-0.047-0.01012.3410.0380.0380.0000.0000.0000.000
75B85LEU00.0210.02713.989-0.006-0.0060.0000.0000.0000.000
76B86HIS0-0.0130.00113.8660.0420.0420.0000.0000.0000.000
77B87PHE00.0510.00918.1290.0220.0220.0000.0000.0000.000
78B88ALA0-0.0060.00421.646-0.003-0.0030.0000.0000.0000.000
79B89THR00.0360.01723.3080.0150.0150.0000.0000.0000.000
80B90PRO0-0.035-0.02826.874-0.005-0.0050.0000.0000.0000.000
81B91MET0-0.0030.01529.8200.0010.0010.0000.0000.0000.000
82B92ASP-1-0.792-0.89231.627-0.087-0.0870.0000.0000.0000.000
83B93PRO00.030-0.00934.490-0.003-0.0030.0000.0000.0000.000
84B94LEU0-0.0220.00635.659-0.002-0.0020.0000.0000.0000.000
85B95PHE00.0610.01835.4180.0020.0020.0000.0000.0000.000
86B96LEU0-0.003-0.00330.465-0.001-0.0010.0000.0000.0000.000
87B97LEU0-0.044-0.02035.131-0.001-0.0010.0000.0000.0000.000
88B98LEU00.0090.01538.3260.0030.0030.0000.0000.0000.000
89B99HIS00.0710.02635.4530.0070.0070.0000.0000.0000.000
90B100TYR0-0.0090.01139.2050.0010.0010.0000.0000.0000.000
91B101LEU0-0.011-0.00840.7180.0040.0040.0000.0000.0000.000
92B102LEU0-0.005-0.00740.7230.0030.0030.0000.0000.0000.000
93B103LYS10.8690.92638.2600.1130.1130.0000.0000.0000.000
94B104ALA00.0330.03544.2660.0030.0030.0000.0000.0000.000
95B105GLY00.0240.01747.1650.0030.0030.0000.0000.0000.000
96B106LYS10.8990.95148.8090.0680.0680.0000.0000.0000.000
97B123PRO00.030-0.00629.3720.0040.0040.0000.0000.0000.000
98B124ASP-1-0.797-0.89226.997-0.195-0.1950.0000.0000.0000.000
99B125CYS0-0.039-0.03930.5450.0080.0080.0000.0000.0000.000
100B126THR00.0130.01433.7240.0070.0070.0000.0000.0000.000
101B127LEU0-0.003-0.00629.2390.0090.0090.0000.0000.0000.000
102B128LEU0-0.029-0.00631.7660.0050.0050.0000.0000.0000.000
103B129LEU00.0430.01633.4310.0030.0030.0000.0000.0000.000
104B130ARG10.8950.96134.3110.1040.1040.0000.0000.0000.000
105B131PHE00.004-0.00331.895-0.001-0.0010.0000.0000.0000.000
106B132PRO00.0330.00137.5350.0030.0030.0000.0000.0000.000
107B133GLU-1-0.826-0.90739.910-0.061-0.0610.0000.0000.0000.000
108B134LEU00.0150.03040.4570.0010.0010.0000.0000.0000.000
109B135GLU-1-0.806-0.88641.825-0.056-0.0560.0000.0000.0000.000
110B136LYS10.8700.91545.0880.0560.0560.0000.0000.0000.000
111B137SER0-0.0310.00540.5700.0010.0010.0000.0000.0000.000
112B138LEU00.0450.00742.0640.0000.0000.0000.0000.0000.000
113B139ARG10.8570.90744.6180.0540.0540.0000.0000.0000.000
114B140HIS00.0170.00745.2310.0020.0020.0000.0000.0000.000
115B141VAL00.0110.01243.6230.0010.0010.0000.0000.0000.000
116B142THR0-0.072-0.02945.2500.0000.0000.0000.0000.0000.000
117B143GLU-1-0.815-0.90147.979-0.053-0.0530.0000.0000.0000.000
118B151LYS11.0221.01250.4800.0520.0520.0000.0000.0000.000
119B152TYR0-0.055-0.03550.710-0.002-0.0020.0000.0000.0000.000
120B153TYR00.0270.01546.6510.0000.0000.0000.0000.0000.000
121B154LYS10.8980.93949.5420.0570.0570.0000.0000.0000.000
122B155TYR00.0370.00845.7390.0000.0000.0000.0000.0000.000
123B156SER0-0.011-0.02048.9540.0040.0040.0000.0000.0000.000
124B157SER00.0950.05249.300-0.002-0.0020.0000.0000.0000.000
125B158GLU-1-0.788-0.87750.200-0.051-0.0510.0000.0000.0000.000
126B159LYS10.8360.92450.2460.0560.0560.0000.0000.0000.000
127B160THR0-0.002-0.01344.964-0.002-0.0020.0000.0000.0000.000
128B161LEU00.0030.02046.719-0.002-0.0020.0000.0000.0000.000
129B162LYS10.8470.90648.4060.0490.0490.0000.0000.0000.000
130B163TRP0-0.077-0.03839.5110.0010.0010.0000.0000.0000.000
131B164LEU00.0390.01142.053-0.001-0.0010.0000.0000.0000.000
132B165GLU-1-0.704-0.82944.527-0.056-0.0560.0000.0000.0000.000
133B166LYS10.8610.94645.2800.0620.0620.0000.0000.0000.000
134B167LYS10.8510.92938.8440.0830.0830.0000.0000.0000.000
135B168VAL00.0450.03541.815-0.002-0.0020.0000.0000.0000.000
136B169ASN0-0.047-0.03843.4930.0020.0020.0000.0000.0000.000
137B170GLN0-0.033-0.02040.519-0.001-0.0010.0000.0000.0000.000
138B171THR0-0.013-0.02537.8840.0000.0000.0000.0000.0000.000
139B172VAL00.0240.00940.3130.0000.0000.0000.0000.0000.000
140B173VAL0-0.028-0.00742.6670.0020.0020.0000.0000.0000.000
141B174ALA0-0.010-0.00537.4680.0010.0010.0000.0000.0000.000
142B175LEU0-0.006-0.00737.1350.0000.0000.0000.0000.0000.000
143B176LYS10.8040.89439.2360.0500.0500.0000.0000.0000.000
144B177ALA0-0.031-0.00839.6140.0020.0020.0000.0000.0000.000
145B178ASN0-0.049-0.03135.1050.0040.0040.0000.0000.0000.000
146B179ASN0-0.0110.00236.349-0.002-0.0020.0000.0000.0000.000
147B180VAL0-0.0050.00234.907-0.001-0.0010.0000.0000.0000.000
148B181ASN0-0.054-0.01637.1010.0030.0030.0000.0000.0000.000
149B203GLU-1-0.796-0.88448.164-0.047-0.0470.0000.0000.0000.000
150B204ASP-1-0.864-0.93144.933-0.053-0.0530.0000.0000.0000.000
151B205TYR00.0900.02741.757-0.002-0.0020.0000.0000.0000.000
152B206VAL0-0.048-0.01643.758-0.003-0.0030.0000.0000.0000.000
153B207ARG10.8100.89644.6970.0500.0500.0000.0000.0000.000
154B208TYR00.0280.02135.438-0.004-0.0040.0000.0000.0000.000
155B209ALA00.010-0.00839.751-0.005-0.0050.0000.0000.0000.000
156B210HIS0-0.038-0.02040.310-0.003-0.0030.0000.0000.0000.000
157B211GLY00.0350.02139.027-0.003-0.0030.0000.0000.0000.000
158B212LEU00.0090.01434.525-0.005-0.0050.0000.0000.0000.000
159B213ILE0-0.039-0.01535.671-0.005-0.0050.0000.0000.0000.000
160B214SER00.0340.01037.156-0.005-0.0050.0000.0000.0000.000
161B215ASP-1-0.899-0.93732.117-0.130-0.1300.0000.0000.0000.000
162B216TYR0-0.136-0.09030.118-0.010-0.0100.0000.0000.0000.000
163B217ILE0-0.056-0.03534.7860.0020.0020.0000.0000.0000.000
164B218PRO00.0530.04037.5230.0030.0030.0000.0000.0000.000
165B219LYS10.7550.85839.2950.0770.0770.0000.0000.0000.000
166B220GLU-1-0.762-0.88440.413-0.079-0.0790.0000.0000.0000.000
167B221LEU0-0.0040.00139.8380.0030.0030.0000.0000.0000.000
168B222SER0-0.035-0.02043.4230.0040.0040.0000.0000.0000.000
169B223ASP-1-0.800-0.88444.719-0.069-0.0690.0000.0000.0000.000
170B224ASP-1-0.833-0.90545.534-0.069-0.0690.0000.0000.0000.000
171B225LEU0-0.016-0.00546.8610.0030.0030.0000.0000.0000.000
172B226SER0-0.045-0.02947.5830.0030.0030.0000.0000.0000.000
173B227LYS10.8460.91443.1040.0760.0760.0000.0000.0000.000
174B228PHE00.0200.00948.0100.0020.0020.0000.0000.0000.000
175B229LEU0-0.005-0.01051.0740.0020.0020.0000.0000.0000.000
176B230LYS10.8140.90249.2470.0550.0550.0000.0000.0000.000
177B231LEU0-0.037-0.00950.929-0.002-0.0020.0000.0000.0000.000